Stop-Motion Workshop

Tools:

Dragon stop-motion (pro, $$$)
istopmotion (mac, $$)
MokeyJam (Windows, free) | no special program needed! Just a camera.
Stop-motion Max/MSP app and patch by Graham Wakefield, re-worked by yours truly

Examples:

The Brothers Quay
The Bead Game
Aanaatt
A Game with Stones
Bottle
Deadline
The Deep
Believer